We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully 13C-labeled and non-labeled plants and LC–MS/MS. Our approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $20.17 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
All program packages and source codes are freely available at http://prime.psc.riken.jp/.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This work was partially supported by KAKENHI (JSPS 15K01812 (H.T.), 15H05897 (M.A.), 16H06454 (M.Y.), 17H03621 (M.A.), 18H02432 (H.T.), 18K19155 (H.T.); MHLW 30190401 (M.A.)), MAFF Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry (R.N.), JST the Strategic International Research Cooperative Program (R.N.), JST National Bioscience Database Center (M.A.), JST the Strategic International Collaborative Research Program (K.S.), Chiba University the GP Program (K.S.) and the Japan Advanced Plant Science Network (K.S.). We thank the HMDB, LipidMAPS and PMN consortiums for providing the SDF files; ChemAxon for a free research license for the Marvin and JChem cheminformatics tools; K. Yonekura-Sakakibara, Y. Higashi, Y. Sawada and K. Mochida for discussions on plant metabolomics; M. Yokota Hirai for providing the place for compound synthesis (RIKEN CSRS); S. Tsugawa for data curation (RIKEN IMS); and U. Petralia for English editing. This work was also supported by the Centre of BioSystems Genomics (no. AA3-WU-PL) (R.K.), the ‘Learning from Nature’ program funded by the Dutch Technology Foundation (STW grant number 10996), which is part of the Netherlands Organization for Scientific Research (J.A.B.-M.), the European Plant Phenotyping Network (EPPN, grant agreement no. 284443) funded by the FP7 Research Infrastructures Program of the European Union (J.A.B.-M.) and the NUE-CROPS project (grant agreement no. 222645) funded by the FP7-CP-IP Research Infrastructures Program of the European Union (N.O.-E.).